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While employed on the campus of Swansea University, Cox installed a very early version of Linux on one of the machines belonging to the university computer society. This was one of the first Linux installations on a busy network and revealed many bugs in the networking code. Cox fixed many of these bugs and went on to rewrite much of the networking subsystem. He then became one of the main developers and maintainers of the whole kernel.

He maintained the 2.2 branch, and his own versions of the 2.4 branch (signified by an "ac" in the version, for example 2.4.13-ac1). This branch was very stable and contained bugfixes that went directly into the vendor kernels. He was once commonly regarded as being the "second in command" after Linus Torvalds himself, before reducing his involvement with Linux to study for an MBA.[1]

On 28 July 2009, Cox relinquished his role as the TTY layer maintainer, after receiving criticism from Torvalds.[2][3]

Alan was employed by the Linux distributor Red Hat during 1999-2009.[4] Starting from 2011 he was employed by Intel Corporation, but left both Intel and Linux kernel development in January 2013 "for family reasons".[5]

Alan Cox is an ardent supporter of programming freedom, and an outspoken opponent of software patents, the DMCA and the CBDTPA. He resigned from a subgroup of Usenix in protest, and said he would not visit the United States for fear of being imprisoned after the arrest of Dmitry Sklyarov for DMCA violations.

In January 2007, he applied for a series of patents on "RMS", or rights management systems.[7] It is said that he has filed a patent for digital rights management. Red Hat Inc., Cox's former employer, has stated (in a document drafted by Mark Webbink and Cox himself)[8] that it will not use patents against free software projects.[9]